Crowell, L H, Soneson, Charlotte, Germain, Pierre-Luc, Calini, Daniela, Collin, Ludovic, Raposo, Catarina, Malhotra, Dheeraj, Robinson, D M (2020). “muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data.” Nature Communications, 11(1), 6077. doi:10.1038/s41467-020-19894-4.

Gilis, Jeroen, Perin, Laura, Malfait, Milan, Van den Berge, Koen, Assefa T, Alemu, Verbist, Bie, Risso, Davide, Clement, Lieven (2023). “Differential detection workflows for multi-sample single-cell RNA-seq data.” bioRxiv. doi:10.1101/2023.12.17.572043.

Germain, Pierre-Luc, Robinson, D M (2025). “Bulk-based hypothesis weighing to increase power in single-cell differential expression analysis.” bioRxiv. doi:10.1101/2025.04.15.648932.